Public Health England SNP calling Pipeline (PHEnix)

This documentation is designed to give an overview as well as detailed API reference for Public Health England’s single nucleotide polymorphism calling pipeline. Currently the pipeline does not provide stand alone means of calling SNPs, instead it interfaces with other published tool e.g. BWA and samtools.

Contents:

• Introduction
  • Installation
  • Overview
  • Requirements
  • Python
  • 3rd Party Requirements
  • Samtools
  • BCFTools
  • Picard Tools
• Prerequisites
• Filters
• Annotators
• Calling SNPs
  • Config
• Converting to FASTA
• API Reference
  • Filters
  • Mappers
  • Variant Callers
• Scripts
  • phenix
• Galaxy
  • Primer
  • How to get your own Galaxy server:
  • How to install Phenix to your Galaxy server:
  • How to use Phenix on Galaxy:
  • Advanced - Changing the Phenix vcf filtering settings:

Indices and tables

• Index
• Module Index
• Search Page